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- PDB-6uuf: Crystal structure of a Nudix Hydrolase from M. Smegmatis, RenU -

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Basic information

Entry
Database: PDB / ID: 6uuf
TitleCrystal structure of a Nudix Hydrolase from M. Smegmatis, RenU
ComponentsNudix Hydrolase, RenU
KeywordsHYDROLASE / Nudix hydrolase / NADHase / mutt3
Function / homologyNUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / hydrolase activity / Mutator protein MutT3 (MutT/nudix family)
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWright, K.M. / Yoder, J. / Shoemaker, S. / Hernandez, A. / Iheanacho, A. / Marques, I. / Amzel, M.L. / Gabelli, S.B.
CitationJournal: To Be Published
Title: Structure of RenU
Authors: Wright, K.M. / Yoder, J. / Shoemaker, S. / Hernandez, A. / Iheanacho, A. / Marques, I. / Amzel, M.L. / Nguyen, L. / Gabelli, S.B.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nudix Hydrolase, RenU
B: Nudix Hydrolase, RenU


Theoretical massNumber of molelcules
Total (without water)35,7282
Polymers35,7282
Non-polymers00
Water1,49583
1
A: Nudix Hydrolase, RenU


Theoretical massNumber of molelcules
Total (without water)17,8641
Polymers17,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nudix Hydrolase, RenU


Theoretical massNumber of molelcules
Total (without water)17,8641
Polymers17,8641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.198, 118.738, 36.432
Angle α, β, γ (deg.)90.000, 92.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nudix Hydrolase, RenU / Putative mutator protein MutT3 (MutT/nudix family)


Mass: 17864.029 Da / Num. of mol.: 2 / Mutation: E74A, E77A, E78A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: mutT3, MSMEI_0773 / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FED3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1-1.4 M NaAc, 0.1 M BTP pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.93927 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.1→59.37 Å / Num. obs: 15812 / % possible obs: 93.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.047 / Rrim(I) all: 0.087 / Χ2: 1.516 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.60.1776330.9610.1240.2180.88872.3
2.14-2.182.80.1696210.9670.1170.2060.87979.5
2.18-2.222.90.1736940.9670.1160.2090.87280
2.22-2.262.90.1696980.9650.1120.2030.97782.9
2.26-2.3130.1667260.9670.110.20.96786.4
2.31-2.3730.1597350.9710.1050.1920.98690.4
2.37-2.4230.1527930.9670.1030.1841.00490.2
2.42-2.493.10.157640.9760.1010.1811.0294.9
2.49-2.563.20.1418660.980.0930.170.96399.2
2.56-2.653.30.1348340.9810.0870.1611.1299.6
2.65-2.743.40.1238410.9850.0790.1461.222100
2.74-2.853.40.1148630.9860.0740.1361.279100
2.85-2.983.20.0998080.9890.0670.121.60199.8
2.98-3.143.20.0848610.990.0560.1011.62599.8
3.14-3.333.40.0818420.9910.0520.0961.873100
3.33-3.593.40.0698380.9920.0440.0822.07599.9
3.59-3.953.20.0628490.9910.0420.0752.46899.8
3.95-4.523.30.0568250.9940.0370.0672.53497.6
4.52-5.73.20.0518600.9960.0330.0612.21599.3
5.7-103.30.0518610.9940.0330.0612.33499.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.397
Highest resolutionLowest resolution
Rotation36.4 Å3.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHJ

3hhj


Resolution: 2.1→59.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.988 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.203
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 683 4.3 %RANDOM
Rwork0.1804 ---
obs0.1828 15093 93.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.01 Å2 / Biso mean: 43.721 Å2 / Biso min: 22.67 Å2
Baniso -1Baniso -2Baniso -3
1-7.53 Å20 Å21.04 Å2
2---3.51 Å20 Å2
3----4.1 Å2
Refinement stepCycle: final / Resolution: 2.1→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 0 83 2455
Biso mean---46.81 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192439
X-RAY DIFFRACTIONr_bond_other_d0.0020.022294
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9213345
X-RAY DIFFRACTIONr_angle_other_deg0.96335230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14822.308104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80915330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7431523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02589
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 36 -
Rwork0.169 843 -
all-879 -
obs--69.21 %

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